Ironclads: One reason would probably be that I almost always play on a pangaea map. I find ironclads useless. I don't need to explore water on pangaea, and I could always use wooden ships to explore if I really needed to. Besides, destroyers/battleships aren't too far away and they're FAR superior to ironclads. Plus, since ironclads are an optional tech in C3C, it'd be a waste of precious research. By the time you automatically get them, you should have destroyers/battleships.
Horsemen: Horsemen are meant for offense, and swordsmen have them beat by a full attack point. Sure, swordsmen don't have the double movement range, but in the ancient ages, I'd wage war on a close neighbor rather than someone across the map. Besides, I do most of my conquering when I've switched to Monarchy, and by that time knights aren't that far away. By the time I really mobilize for war, I will have found and secured a source of iron.
Longbowmen: Alright, usually, I would use knights over both Medieval infantry and Longbowmen, but if there were no horses, I would go for MDIs. The two defense can be useful if you don't want to bring along pikemen when conquering cities, and the bombardment is only useful if you have a large number of longbows. Too large to be worth it.
Chariots: A warrior on wheels. I'd rather use swordsmen/spearmen for offense and defense respectively.
Stealth Fighter: The abillity to be virtually invisible is negated by it's low bombardment value. Besides, I tend to use air units to attack stacks of units rather than cities, and stacks rarely have flaks. I use RAs for city bombardment, or whatever the current artillery is.
Cruise Missile: The fact that it's one-time only just doesn't appeal to me. Even with high bombardment value, low cost, and ability to kill on bombardment. I'd rather bring along artillery/RA as they're reusable.
Marines: Tanks are better. What else can I say? I don't care much for being able to attack from a carrier. I'd rather unload some tanks/infantry near a city and attack the next turn. Being able to pull off amphibious attack doesn't add any element of surprise or anything. Your enemies will notice your transports in their territory, so I'd rather unload tanks.
Flak: Enemies rarely use air units anyway.
Paratrooper: Like amphibious attack. A pretty useless ability. Rarely does the enemy make a wall of troops that you can't pass through, and if they did, they'd have to spread their troops out pretty thinly, making the wall easy to breach.
I'll add more if I feel like it.